The enteroendocrine cells, which comprise approximately 1% of epithelial cells in the gastrointestinal tract, represent the largest population of hormone-producing cells in the body. The enteroendocrine cells share a common lineage with other non-endocrine cell lineages and originate from primitive intestinal stem cells in the intestinal crypts. There are two complementary populations of stem cells, a self-renewing stem cell population and a quiescent stem cell population. The self-renewing stem cells highly express Lgr5 and reside between Paneth cells at the crypt base where Wnt signaling is active whereas quiescent stem cells express Bmi1 and reside at the position 4. Thus the lineage-specific precursor cells are thought to differentiate immediately from the self-renewing Lgr5+ cells. Endocrine precursor cells differentiate toward mature hormone-producing endocrine cells that are classified into at least 15 different terminally differentiated lineages (or subsets) by their expression of specific peptide hormones. Although the molecular mechanisms that regulate the differentiation from the endocrine precursor cells have not been fully characterized, key transcription factors have been implicated in enteroendocrine cell differentiation (Pax4, Pax6, BETA2/NeuorD, Pdx1, Gfi, Nkx2.2 and Sox9). There is a relationship between spatial orientation of the enteroendocrine cells and their differentiation process. Previous reports on characterization of entroendocrine cell differentiation using BrdU incorporation, morphological and immunohistochemical methods demonstrated that the majority of enteroendocrine cells complete the differentiation process within the crypt and migrate upward along the villus as mature hormone-producing cells. However, a small population of enteroendocrine cells migrates downward to the bottom of the crypt. Enteroendocrine cells are comprised of subsets, whose differentiation is determined by specific transcription factors that regulate both the specific co-expression of hormones and their location within the crypt-villus axis. The differentiation signaling pathways mediated by Wnt, Hedgehog, Notch, BMP and EphB/ephrin are restricted spatially along the crypt-villus axis in the epithelium and the mesenchyme of the intestine. Below position +4 (where the self-renewing Lgr5+ stem cells reside with Paneth cells) in the crypt, Wnt-signaling is especially active . Presently, it is unclear what determines whether a subset of enteroendocrine cells remains in the Wnt signaling rich area instead of migrating up to the villi and why. This subset of enteroendocrine cells that resides at the crypt base has become our particular interest especially since we are able to visualize GFP+ enteroendocrine cells at the crypt base in the genetically engineered animals that express GFP under the control of the cholecystokinin (CCK) gene promoter. In addition, the technique recently developed to make cultured organoids enables us to trace migration patterns of GFP-expressing endocrine cells along the crypt-villus axis. By taking advantage of GFP expression, we examined CCK-GFP-expressing cells for expression of differentiation markers and migration patterns in freshly isolated primary crypts and cultured organoid system, respectively, to characterize the subset at the crypt base using the CCK-GFP transgenic animals. We found that the subset of endocrine cells at the crypt base resides at this Wnt signaling-active zone after its downward migration from around position+4 region and expresses both stem and post-mitotic mature endocrine cell markers and that this subset is at least phenotypically different from other subsets of enteroendocrine cells which migrate upward to the villi.